Genomic Surveillance of SARS-CoV-2 Variants Circulating in Rajasthan in 2025.

Area of Science:

• Virology
• Genomics
• Epidemiology

Background:

• The COVID-19 pandemic, caused by SARS-CoV-2, has seen significant viral evolution, leading to variants with altered transmissibility and immune escape properties.
• Understanding the genetic landscape of circulating SARS-CoV-2 strains is vital for effective public health interventions.

Purpose of the Study:

• To identify and characterize SARS-CoV-2 variants in Jaipur, India, during a specific period.
• To assess the epidemiological features and implications of identified variants for public health.

Main Methods:

• Next-generation sequencing was performed on 373 SARS-CoV-2 positive samples with Ct values ≤ 25.
• Samples were collected from patients in Jaipur, India, between April 30, 2025, and September 5, 2025.

Main Results:

• The XFG lineage was the predominant variant (48.8%), including sublineages XFG.3 and XFG.3.1. Other identified lineages included PY.1, LF.7, and JN.1.
• The majority of positive cases (88.47%) were vaccinated. Reinfection was observed in 28.95% of cases.
• Symptomatic cases (78.82%) and comorbidities (25.74%) were noted, with 25.47% requiring hospitalization and three deaths.

Conclusions:

• The XFG variant, a recombinant of LF.7 and LP.8.1.2 Omicron subvariants, was associated with the highest surge in COVID-19 cases.
• Sustained genomic surveillance in Rajasthan is essential for real-time tracking of viral evolution, risk mitigation, and preparedness.
• Findings have implications for refining public health responses and vaccination strategies in the region.